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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Publications at this Location » Publication #400512

Research Project: Genetic Improvement and Cropping Systems of Alfalfa for Livestock Utilization, Environmental Protection and Soil Health

Location: Plant Science Research

Title: Mapping disease resistance genes in alfalfa

item Samac, Deborah - Debby
item MEDINA, CESAR - University Of Minnesota
item Yu, Long-Xi
item SIERRA-MOYA, YEIDYMAR - University Of Minnesota
item ZHAO, DONGYAN - Cornell University
item LIN, MENG - Cornell University
item MEJIA-GUERRA, KATHERINE - Cornell University
item BEIL, CRAIG - Cornell University
item SHEEHAN, MOIRA - Cornell University

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 12/7/2022
Publication Date: 1/13/2023
Citation: Samac, D.A., Medina, C.A., Yu, L., Sierra-Moya, Y., Zhao, D., Lin, M., Mejia-Guerra, K., Beil, C., Sheehan, M. 2023. Mapping disease resistance genes in alfalfa. Plant and Animal Genome. January 13-18, 2023. San Diego, California.

Interpretive Summary:

Technical Abstract: Developing new alfalfa cultivars requires the screening of thousands of plants for diverse disease resistant traits to identify plants with resistance to multiple diseases. Modern cultivars have resistance to widespread diseases including Phytophthora root rot, bacterial wilt, Fusarium wilt, Verticillium wilt, anthracnose, and Aphanomyces root rot. Surveys indicate that resistance to emerging disease problems are needed beyond those already found in current cultivars. Additionally, forage yields and productive stand life could be increased by developing cultivars with high numbers of plants with resistance to the major diseases. However, obtaining cultivars with greater than 50% of plants resistant to each disease is difficult using recurrent phenotypic selection. Mapping of genes for race-specific resistance to Aphanomyces root rot was done to help clarify the race/resistance gene relationships and facilitate breeding for resistance. An F1 population that showed segregation for resistance to race 1 and to race 2 was used for genotyping-by-sequencing (GBS) followed by genotype calling using FreeBayes pipelines. Subsequently, resistance was mapped in F1 plants and a backcross population using DArTag markers. Both platforms identified SNP markers significantly associated with resistance to race 1 on chromosome 1 with candidate NBS-LRR genes within 38 kbp. Markers associated with resistance to race 2 were identified on chromosome 2 with allele-specific SNPs for race 2 resistance identified with DArTag. Recently, bacterial stem blight of alfalfa has emerged as a yield-reducing disease multiple locations across the United States. Most alfalfa cultivars have low levels of resistance to bacterial stem blight. A reciprocal F1 mapping approach was taken to identify QTLs for resistance to this disease. GBS followed by genotype calling using the NGSEP pipeline was used for generating the genomic matrix. The phenotypic responses were modeled using a linear mixed model including the genomic relationship matrix to obtain the genomic best linear unbiased prediction (GBLUP) values. Finally, GBLUP values and the genomic matrix were used in genome-wide association studies (GWAS) to identify markers associated with resistance to bacterial stem blight. A total of 14 significant markers (FDR > 0.05) were identified, several in genes with reported roles in plant defense.